Comparison of pattern detection methods in microarray time series of the segmentation clock

PLoS ONE

Volumn 3, Issue 8, 2008, Pages

  Dequéant, Mary Lee ^a   Ahnert, Sebastian ^b   Edelsbrunner, Herbert ^c,d,e   Fink, Thomas M A ^f,g,h   Glynn, Earl F ^a   Hattem, Gaye ^a   Kudlicki, Andrzej ⁱ   Mileyko, Yuriy ^c   Morton, Jason ^j   Mushegian, Arcady R ^a   Pachter, Lior ^j   Rowicka, Maga ⁱ   Shiu, Anne ^j   Sturmfels, Bernd ^j   Pourquié, Olivier ^a,k  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c Duke University   (United States)

^d DUKE UNIVERSITY   (United States)

^e Geomagic   (United States)

^f INSERM U900   (France)

^g INSTITUT CURIE   (France)

^h PSL RESEARCH UNIVERSITY   (France)

ⁱ UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k HOWARD HUGHES MEDICAL INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE RICH PROTEIN 61; WNT PROTEIN; CYR61 PROTEIN, MOUSE; NOTCH RECEPTOR; UNCLASSIFIED DRUG;

ADDRESS REDUCTION; ARTICLE; CYCLOHEDRON; DATA ANALYSIS; EMBRYO; EMBRYO SEGMENTATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC DATABASE; GENETIC TRANSCRIPTION; INTERMETHOD COMPARISON; MATHEMATICAL GENETICS; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; PHASE CONSISTENCY; STABLE PERSISTENCE; TIME SERIES ANALYSIS; ANIMAL; ANIMAL EMBRYO; CELL CYCLE; DNA MICROARRAY; DNA PROBE; EMBRYO DEVELOPMENT; GENE EXPRESSION REGULATION; GENETICS; GENOME; PATTERN RECOGNITION; PHYSIOLOGY;

ANIMALS; CELL CYCLE; CYSTEINE-RICH PROTEIN 61; DNA PROBES; EMBRYO, MAMMALIAN; EMBRYONIC DEVELOPMENT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, PHYSIOLOGICAL; RECEPTORS, NOTCH; WNT PROTEINS;

EID: 51349152854     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002856     Document Type: Article

References (35)

1. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
2. McDonald MJ, Rosbash M (2001) Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107: 567-578.
3. Claridge-Chang A, Wijnen H, Naef F, Boothroyd C, Rajewsky N, et al. (2001) Circadian regulation of gene expression systems in the Drosophila head. Neuron 32: 657-671.
4. Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, et al. (2003) The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum. PLoS Biol 1: E5.
5. Dequeant ML, Glynn E, Gaudenz K, Wahl M, Chen J, et al. (2006) A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science 314: 1595-1598.
6. Palmeirim I, Henrique D, Ish-Horowicz D, Pourquié O (1997) Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell 91: 639-648.
7. Dequeant ML, Pourquie O (2008) Segmental patterning of the vertebrate embryonic axis. Nat Rev Genet 9: 370-382.
8. McGrew MJ, Dale JK, Fraboulet S, Pourquie O (1998) The lunatic fringe gene is a target of the molecular clock linked to somite segmentation in avian embryos. Curr Biol 8: 979-982.
9. Aulehla A, Johnson RL (1999) Dynamic expression of lunatic fringe suggests a link between notch signaling and an autonomous cellular oscillator driving somite segmentation. Dev Biol 207: 49-61.
10. Forsberg H, Crozet F, Brown NA (1998) Waves of mouse Lunatic fringe expression, in four-hour cycles at two-hour intervals, precede somite boundary formation. Curr Biol 8: 1027-1030.
11. Glynn EF, Chen J, Mushegian AR (2006) Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics 22: 310-316.
12. Edelsbrunner H, Letscher D, Zomorodian A (2002) Topological persistence and simplification. Discrete Comput Geom 28: 511-533.
13. Ahnert SE, Fink TMA (2006) New distance measure for microarray data series based on unbiased pattern detection. Bioinformatics. pp 1-4.
14. Fink TM, Brown FCS, Willbrand K (2007) 1-D random landscapes and non-random data series. Europhysics Letters (EPL) 79: 38006.
15. Morton J, Pachter L, Shiu A, Sturmfels B (2007) The cyclohedron test for finding periodic genes in time course expression studies. Stat Appl Genet Mol Biol 6: Article 21.
16. Morton J, Pachter L, Shiu A, Sturmfels B, Wienand O (2006) Geometry of rank tests. Proceedings of the conference Probabilistic Graphical Models (PGM 3), Prague, Czech Republic, September 2006, available from ArXiv:math.ST/0605173.
17. Aulehla A, Wehrle C, Brand-Saberi B, Kemler R, Gossler A, et al. (2003) Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev Cell 4: 395-406.
18. Suriben R, Fisher DA, Cheyette BN (2006) Dact1 presomitic mesoderm expression oscillates in phase with Axin2 in the somitogenesis clock of mice. Dev Dyn 235: 3177-3183.
19. Jouve C, Palmeirim I, Henrique D, Beckers J, Gossler A, et al. (2000) Notch signalling is required for cyclic expression of the hairy-like gene HES1 in the presomitic mesoderm. Development 127: 1421-1429.
20. Ishikawa A, Kitajima S, Takahashi Y, Kokubo H, Kanno J, et al. (2004) Mouse Nkd1, a Wnt antagonist, exhibits oscillatory gene expression in the PSM under the control of Notch signaling. Mech Dev 121: 1443-1453.
21. Leimeister C, Dale K, Fischer A, Klamt B, Hrabe de Angelis M, et al. (2000) Oscillating expression of c-hey2 in the presomitic mesoderm suggests that the segmentation clock may use combinatorial signaling through multiple interacting bHLH factors. Dev Biol 227: 91-103.
22. Dunwoodie SL, Clements M, Sparrow DB, Sa X, Conlon RA, et al. (2002) Axial skeletal defects caused by mutation in the spondylocostal dysplasia/pudgy gene D113 are associated with disruption of the segmentation clock within the presomitic mesoderm. Development 129: 1795-1806.
23. Lin SM, McConnell P, Johnson KF, Shoemaker J (2004) MedlineR: an open source library in R for Medline literature data mining. Bioinformatics 20: 3659-3661.
24. Latinkic BV, Mercurio S, Bennett B, Hirst EM, Xu Q, et al. (2003) Xenopus Cyr61 regulates gastrulation movements and modulates Wnt signalling. Development 130: 2429-2441.
25. Lickert H, Cox B, Wehrle C, Taketo MM, Kemler R, et al. (2005) Dissecting Wnt/beta-catenin signaling during gastrulation using RNA interference in mouse embryos. Development 132: 2599-2609.
26. Malliri A, Collard JG (2003) Role of Rho-family proteins in cell adhesion and cancer. Curr Opin Cell Biol 15: 583-589.
27. Feng Y, Bommer GT, Zhai Y, Akyol A, Hinoi T, et al. (2007) Drosophila split ends homologue SHARP functions as a positive regulator of Wnt/ beta-catenin/T-cell factor signaling in neoplastic transformation. Cancer Res 67: 482-491.
28. Schwartz DR, Wu R, Kardia SL, Levin AM, Huang CC, et al. (2003) Novel candidate targets of beta-catenin/T-cell factor signaling identified by gene expression profiling of ovarian endometrioid adenocarcinomas. Cancer Res 63: 2913-2922.
29. Si W, Kang Q, Luu HH, Park JK, Luo Q, et al. (2006) CCN1/Cyr61 is regulated by the canonical Wnt signal and plays an important role in Wnt3A-induced osteoblast differentiation of mesenchymal stem cells. Mol Cell Biol 26: 2955-2964.
30. Kudlicki A, Rowicka M, Otwinowski Z (2007) SCEPTRANS: an online tool for analyzing periodic transcription in yeast. Bioinformatics 23: 1559-1561.
31. Ahnert SE, Willbrand K, Brown FC, Fink TM (2006) Unbiased pattern detection in microarray data series. Bioinformatics 22: 1471-1476.
32. Cohen-Steiner D, Edelsbrunner H, Harer J, Mileyko Y (2007) Lipschitz functions have Lp-stable persistence, manuscript, Department of Computer Science, Duke University, Durham, North Carolina.
33. Yeung KY, Haynor DR, Ruzzo WL (2001) Validating clustering for gene expression data Bioinformatics 17: 309-318.
34. Clewley RH, Guckenheimer JM, Valero-Cuevas FJ (2008) Estimating effective degrees of freedom in motor systems. IEEE Trans Biomed Eng 55: 430-442.
35. Henrique D, Adam J, Myat A, Chitnis A, Lewis J, et al. (1995) Expression of a Delta homologue in prospective neurons in the chick. Nature 375: 787-790.